\chapter{Visualization}

During a simulation, \brahms generates the file {\tt trajectory.pdb}, which can be visualized using standard molecular viewers. In the \brahms package, there is a directory ({\tt exampleSimulations/2-membraneSystems/vmdStateFiles}) containing some example files that can be used to optimize visualization with the popular program VMD.~\citep{HUMP96} For example, from a simulation directory, start VMD, then click on {\tt File | Load state...} and then load one of the example state files. VMD also lets you define ``favorite'' directories where you can store frequently-used status files for easy access.
An example for the kind of images you can produce is given in Figure~\ref{fig:snap}.
\begin{figure}[ht]
\centering
\includegraphics[scale=0.5]{visualization/snap.eps}
\caption[Bilayer snapshot]{Bilayer snapshot. Visualization of a system comprising 128 DOPC lipids and 4232 water molecules.}
\label{fig:snap}
\end{figure}


